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Murray JE, Valli E, Milazzo G, Mayoh C, Gifford AJ, Fletcher JI, Xue C, Jayatilleke N, Salehzadeh F, Gamble LD, Rouaen JRC, Carter DR, Forgham H, Sekyere EO, Keating J, Eden G, Allan S, Alfred S, Kusuma FK, Clark A, Webber H, Russell AJ, de Weck A, Kile BT, Santulli M, De Rosa P, Fleuren EDG, Gao W, Wilkinson-White L, Low JKK, Mackay JP, Marshall GM, Hilton DJ, Giorgi FM, Koster J, Perini G, Haber M, Norris MD. The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis. Nat Commun 2024; 15:5585. [PMID: 38992040 PMCID: PMC11239676 DOI: 10.1038/s41467-024-49871-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/23/2024] [Indexed: 07/13/2024] Open
Abstract
MYCN oncogene amplification is frequently observed in aggressive childhood neuroblastoma. Using an unbiased large-scale mutagenesis screen in neuroblastoma-prone transgenic mice, we identify a single germline point mutation in the transcriptional corepressor Runx1t1, which abolishes MYCN-driven tumorigenesis. This loss-of-function mutation disrupts a highly conserved zinc finger domain within Runx1t1. Deletion of one Runx1t1 allele in an independent Runx1t1 knockout mouse model is also sufficient to prevent MYCN-driven neuroblastoma development, and reverse ganglia hyperplasia, a known pre-requisite for tumorigenesis. Silencing RUNX1T1 in human neuroblastoma cells decreases colony formation in vitro, and inhibits tumor growth in vivo. Moreover, RUNX1T1 knockdown inhibits the viability of PAX3-FOXO1 fusion-driven rhabdomyosarcoma and MYC-driven small cell lung cancer cells. Despite the role of Runx1t1 in MYCN-driven tumorigenesis neither gene directly regulates the other. We show RUNX1T1 forms part of a transcriptional LSD1-CoREST3-HDAC repressive complex recruited by HAND2 to enhancer regions to regulate chromatin accessibility and cell-fate pathway genes.
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Affiliation(s)
- Jayne E Murray
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Emanuele Valli
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
- Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Chengyuan Xue
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Nisitha Jayatilleke
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Firoozeh Salehzadeh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Laura D Gamble
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Jourdin R C Rouaen
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Daniel R Carter
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology Sydney, Broadway, NSW, Australia
| | - Helen Forgham
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Eric O Sekyere
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Joanna Keating
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Georgina Eden
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Sophie Allan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Stephanie Alfred
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Frances K Kusuma
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Ashleigh Clark
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Hannah Webber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Amanda J Russell
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Antoine de Weck
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Benjamin T Kile
- Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Martina Santulli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Piergiuseppe De Rosa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Weiman Gao
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Lorna Wilkinson-White
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, NSW, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Jan Koster
- Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia.
- UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia.
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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional regulators with broad expression in the zebrafish spinal cord. Dev Dyn 2024. [PMID: 38850245 DOI: 10.1002/dvdy.717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. RESULTS We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. CONCLUSIONS Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
| | - Paul C Campbell
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, New York, USA
| | - Richard L Bates
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, Syracuse, New York, USA
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Transcription Factors with Targeting Potential in Gliomas. Int J Mol Sci 2022; 23:ijms23073720. [PMID: 35409080 PMCID: PMC8998804 DOI: 10.3390/ijms23073720] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 12/18/2022] Open
Abstract
Gliomas portray a large and heterogeneous group of CNS tumors, encompassing a wide range of low- to high-grade tumors, as defined by histological and molecular characteristics. The identification of signature mutations and other molecular abnormalities has largely impacted tumor classification, diagnosis, and therapy. Transcription factors (TFs) are master regulators of gene expression programs, which ultimately shape cell fate and homeostasis. A variety of TFs have been detected to be aberrantly expressed in brain tumors, being highly implicated in critical pathological aspects and progression of gliomas. Herein, we describe a selection of oncogenic (GLI-1/2/3, E2F1–8, STAT3, and HIF-1/2) and tumor suppressor (NFI-A/B, TBXT, MYT1, and MYT1L) TFs that are deregulated in gliomas and are subsequently associated with tumor development, progression, and migratory potential. We further discuss the current targeting options against these TFs, including chemical (Bortezomib) and natural (Plumbagin) compounds, small molecules, and inhibitors, and address their potential implications in glioma therapy.
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Ding H, Li Y, Zhang Y, Meng H, Wang K, Sun Q, Li X, Dong H, Chen L, He F. Bioinformatics analysis of Myelin Transcription Factor 1. Technol Health Care 2021; 29:441-453. [PMID: 33682781 PMCID: PMC8150646 DOI: 10.3233/thc-218042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND OBJECTIVE: We aimed to further study the role of Myelin Transcription Factor 1(MyT1) in tumor and other diseases and epigenetic regulation, and better understand the regulatory mechanism of MyT1. METHODS: Using bioinformatics analysis, the structure and function of MyT1sequence were predicted and analyzed using bioinformatics analysis, and providing a theoretical basis for further experimental verification and understanding the regulatory mechanism of MyT1. The first, second and third-level structures of MyT1 were predicted and analyzed by bioinformatics analysis tools. RESULTS: MyT1 is found to be an unstable hydrophilic protein, rather than a secretory protein, with no signal peptide or trans-membrane domain; total amino acids located on the surface of the cell membrane. It contains seven zinc finger domains structurally. At sub-cellular level, MyT1 is localized in the nucleus. The phosphorylation site mainly exists in serine, and its secondary structure is mainly composed of random coils and alpha helices; the three-dimensional structure is analyzed by modeling. CONCLUSIONS: In this study, the structure and function of MyT1 protein were predicted, thereby providing a basis for subsequent expression analysis and functional research; it laid the foundation for further investigation of the molecular mechanism involved in the development of diseases.
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Affiliation(s)
- Hongjun Ding
- School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China.,Tianjin Public Security Profession College, Tianjin, China.,School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
| | - Yanju Li
- Medical Laboratory Department, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute, Tianjin, China.,School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
| | - Yanlong Zhang
- School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
| | - Huipeng Meng
- School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
| | - Keqiang Wang
- School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
| | - Qian Sun
- School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
| | - Xichuan Li
- College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Huajiang Dong
- Logistics University of Chinese People's Armed Police Forces, Tianjin, China
| | - Long Chen
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Feng He
- School of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin, China
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Benkafadar N, Janesick A, Scheibinger M, Ling AH, Jan TA, Heller S. Transcriptomic characterization of dying hair cells in the avian cochlea. Cell Rep 2021; 34:108902. [PMID: 33761357 DOI: 10.1016/j.celrep.2021.108902] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/11/2021] [Accepted: 03/03/2021] [Indexed: 12/28/2022] Open
Abstract
Sensory hair cells are prone to apoptosis caused by various drugs including aminoglycoside antibiotics. In mammals, this vulnerability results in permanent hearing loss because lost hair cells are not regenerated. Conversely, hair cells regenerate in birds, making the avian inner ear an exquisite model for studying ototoxicity and regeneration. Here, we use single-cell RNA sequencing and trajectory analysis on control and dying hair cells after aminoglycoside treatment. Interestingly, the two major subtypes of avian cochlear hair cells, tall and short hair cells, respond differently. Dying short hair cells show a noticeable transient upregulation of many more genes than tall hair cells. The most prominent gene group identified is associated with potassium ion conductances, suggesting distinct physiological differences. Moreover, the dynamic characterization of >15,000 genes expressed in tall and short avian hair cells during their apoptotic demise comprises a resource for further investigations toward mammalian hair cell protection and hair cell regeneration.
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Affiliation(s)
- Nesrine Benkafadar
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Amanda Janesick
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mirko Scheibinger
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Angela H Ling
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Taha A Jan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stefan Heller
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Yoon C, Lee D, Lee SJ. Regulation of the Central Dogma through Bioinorganic Events with Metal Coordination for Specific Interactions. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chungwoon Yoon
- Department of Chemistry Institute for Molecular Biology and Genetics, Jeonbuk National University Jeonju 54896 Republic of Korea
| | - Dong‐Heon Lee
- Department of Chemistry Institute for Molecular Biology and Genetics, Jeonbuk National University Jeonju 54896 Republic of Korea
| | - Seung Jae Lee
- Department of Chemistry Institute for Molecular Biology and Genetics, Jeonbuk National University Jeonju 54896 Republic of Korea
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Melhuish TA, Kowalczyk I, Manukyan A, Zhang Y, Shah A, Abounader R, Wotton D. Myt1 and Myt1l transcription factors limit proliferation in GBM cells by repressing YAP1 expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:983-995. [PMID: 30312684 DOI: 10.1016/j.bbagrm.2018.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 12/19/2022]
Abstract
Myelin transcription factor 1 (Myt1) and Myt1l (Myt1-like) are zinc finger transcription factors that regulate neuronal differentiation. Reduced Myt1l expression has been implicated in glioblastoma (GBM), and the related St18 was originally identified as a potential tumor suppressor for breast cancer. We previously analyzed changes in gene expression in a human GBM cell line with re-expression of either Myt1 or Myt1l. This revealed largely overlapping gene expression changes, suggesting similar function in these cells. Here we show that re-expression of Myt1 or Myt1l reduces proliferation in two different GBM cell lines, activates gene expression programs associated with neuronal differentiation, and limits expression of proliferative and epithelial to mesenchymal transition gene-sets. Consistent with this, expression of both MYT1 and MYT1L is lower in more aggressive glioma sub-types. Examination of the gene expression changes in cells expressing Myt1 or Myt1l suggests that both repress expression of the YAP1 transcriptional coactivator, which functions primarily in the Hippo signaling pathway. Expression of YAP1 and its target genes is reduced in Myt-expressing cells, and there is an inverse correlation between YAP1 and MYT1/MYT1L expression in human brain cancer datasets. Proliferation of GBM cell lines is reduced by lowering YAP1 expression and increased with YAP1 over-expression, which overcomes the anti-proliferative effect of Myt1/Myt1l expression. Finally we show that reducing YAP1 expression in a GBM cell line slows the growth of orthotopic tumor xenografts. Together, our data suggest that Myt1 and Myt1l directly repress expression of YAP1, a protein which promotes proliferation and GBM growth.
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Affiliation(s)
- Tiffany A Melhuish
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA; Center for Cell Signaling, University of Virginia, Charlottesville, USA
| | - Izabela Kowalczyk
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA; Center for Cell Signaling, University of Virginia, Charlottesville, USA
| | - Arkadi Manukyan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA; Center for Cell Signaling, University of Virginia, Charlottesville, USA
| | - Ying Zhang
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, USA
| | - Anant Shah
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA; Center for Cell Signaling, University of Virginia, Charlottesville, USA
| | - Roger Abounader
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, USA
| | - David Wotton
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA; Center for Cell Signaling, University of Virginia, Charlottesville, USA.
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Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kariawasam R, Knight M, Gamsjaeger R, Cubeddu L. Backbone 1H, 13C and 15N resonance assignments of the OB domain of the single stranded DNA-binding protein hSSB2 (NABP1/OBFC2A) and chemical shift mapping of the DNA-binding interface. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:107-111. [PMID: 29063999 DOI: 10.1007/s12104-017-9789-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
Single stranded DNA-binding proteins (SSBs) are essential for the maintenance of genome integrity and are required in in all known cellular organisms. Over the last 10 years, the role of two new human SSBs, hSSB1 (NABP2/OBFC2B) and hSSB2 (NABP1/OBFC2A), has been described and characterised in various important DNA repair processes. Both these proteins are made up of a conserved oligonucleotide-binding (OB) fold that is responsible for ssDNA recognition as well a unique flexible carboxy-terminal extension involved in protein-protein interactions. Due to their similar domain organisation, hSSB1 and hSSB2 have been found to display some overlapping functions. However, several studies have also revealed cell- and tissue-specific roles for these two proteins, most likely due to small but significant differences in the protein sequence of the OB domains. While the molecular details of ssDNA binding by hSSB1 has been studied extensively, comparatively little is known about hSSB2. In this study, we use NMR solution-state backbone resonance assignments of the OB domain of hSSB2 to map the ssDNA interaction interface. Our data reveal that ssDNA binding by hSSB2 is driven by four key aromatic residues in analogy to hSSB1, however, some significant differences in the chemical shift perturbations are observed, reflecting differences in ssDNA recognition. Future studies will aim at determining the structural basis of these differences and thus help to gain a more comprehensive understanding of the functional divergences that these novel hSSBs display in the context of genome maintenance.
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Affiliation(s)
- Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Maddison Knight
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia.
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia.
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
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10
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Manukyan A, Kowalczyk I, Melhuish TA, Lemiesz A, Wotton D. Analysis of transcriptional activity by the Myt1 and Myt1l transcription factors. J Cell Biochem 2018; 119:4644-4655. [PMID: 29291346 DOI: 10.1002/jcb.26636] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022]
Abstract
Myt1 and Myt1l (Myelin transcription factor 1, and Myt1-like) are members of a small family of closely related zinc finger transcription factors, characterized by two clusters of C2HC zinc fingers. Both are widely expressed during early embryogenesis, but are largely restricted to expression within the brain in the adult. Myt1l, as part of a three transcription factor mix, can reprogram fibroblasts to neurons and plays a role in maintaining neuronal identity. Previous analyses have indicated roles in both transcriptional activation and repression and suggested that Myt1 and Myt1l may have opposing functions in gene expression. We show that when targeted to DNA via multiple copies of the consensus Myt1/Myt1l binding site Myt1 represses transcription, whereas Myt1l activates. By targeting via a heterologous DNA binding domain we mapped an activation function in Myt1l to an amino-terminal region that is poorly conserved in Myt1. However, genome wide analyses of the effects of Myt1 and Myt1l expression in a glioblastoma cell line suggest that the two proteins have largely similar effects on endogenous gene expression. Transcriptional repression is likely mediated by binding to DNA via the known consensus site, whereas this site is not associated with the transcriptional start sites of genes with higher expression in the presence of Myt1 or Myt1l. This work suggests that these two proteins function similarly, despite differences observed in analyses based on synthetic reporter constructs.
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Affiliation(s)
- Arkadi Manukyan
- Department of Biochemistry and Molecular Genetics, and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
| | - Izabela Kowalczyk
- Department of Biochemistry and Molecular Genetics, and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
| | - Tiffany A Melhuish
- Department of Biochemistry and Molecular Genetics, and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
| | - Agata Lemiesz
- Department of Microbiology, Immunology and Cancer, University of Virginia, Charlottesville, Virginia
| | - David Wotton
- Department of Biochemistry and Molecular Genetics, and Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
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11
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MYT1L mutations cause intellectual disability and variable obesity by dysregulating gene expression and development of the neuroendocrine hypothalamus. PLoS Genet 2017; 13:e1006957. [PMID: 28859103 PMCID: PMC5597252 DOI: 10.1371/journal.pgen.1006957] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/13/2017] [Accepted: 08/04/2017] [Indexed: 12/21/2022] Open
Abstract
Deletions at chromosome 2p25.3 are associated with a syndrome consisting of intellectual disability and obesity. The smallest region of overlap for deletions at 2p25.3 contains PXDN and MYT1L. MYT1L is expressed only within the brain in humans. We hypothesized that single nucleotide variants (SNVs) in MYT1L would cause a phenotype resembling deletion at 2p25.3. To examine this we sought MYT1L SNVs in exome sequencing data from 4, 296 parent-child trios. Further variants were identified through a genematcher-facilitated collaboration. We report 9 patients with MYT1L SNVs (4 loss of function and 5 missense). The phenotype of SNV carriers overlapped with that of 2p25.3 deletion carriers. To identify the transcriptomic consequences of MYT1L loss of function we used CRISPR-Cas9 to create a knockout cell line. Gene Ontology analysis in knockout cells demonstrated altered expression of genes that regulate gene expression and that are localized to the nucleus. These differentially expressed genes were enriched for OMIM disease ontology terms "mental retardation". To study the developmental effects of MYT1L loss of function we created a zebrafish knockdown using morpholinos. Knockdown zebrafish manifested loss of oxytocin expression in the preoptic neuroendocrine area. This study demonstrates that MYT1L variants are associated with syndromic obesity in humans. The mechanism is related to dysregulated expression of neurodevelopmental genes and altered development of the neuroendocrine hypothalamus.
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Viral-mediated overexpression of the Myelin Transcription Factor 1 (MyT1) in the dentate gyrus attenuates anxiety- and ethanol-related behaviors in rats. Psychopharmacology (Berl) 2017; 234:1829-1840. [PMID: 28303373 DOI: 10.1007/s00213-017-4588-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/02/2017] [Indexed: 12/19/2022]
Abstract
RATIONALE Myelin Transcription Factor 1 (MyT1), a member of the Zinc Finger gene family, plays a fundamental role in the nervous system. Recent research has suggested that this transcription factor is associated with the pathophysiology of psychiatric disorders including addiction, schizophrenia, and depression. However, the role of MyT1 in anxiety- and ethanol-related behaviors is still unknown. OBJECTIVES We evaluated the effects of lentiviral-mediated overexpression of MyT1 in the dentate gyrus (DG) on anxiety- and ethanol-related behaviors in rats. METHODS We used the elevated plus maze (EPM) and the open field (OF) tests to assess anxiety-like behavior and a two-bottle choice procedure to measure the effects of MyT1 on ethanol intake and preference. RESULTS MyT1 overexpression produced anxiolytic-like effects in the EPM test and decreased the number of fecal boli in the OF test, without affecting locomotor activity in both behavioral tests. Next, we demonstrated that ethanol intake and preference were decreased in the MyT1-overexpressing rats with no effect on saccharin and quinine, used to assess taste discrimination, and no effect on ethanol clearance suggesting specific alterations in the rewarding effects of ethanol. Most importantly, ectopic MyT1 overexpression increased both MyT1 and BDNF mRNA levels in the DG. Using Pearson's correlation, results showed a strong negative relationship between MyT1 mRNA and anxiety parameters and ethanol consumption and a positive correlation between MyT1 and BDNF mRNAs. CONCLUSION Taken together, MyT1 along with being a key component in anxiety may be a suitable candidate in the search of the molecular underpinnings of alcoholism.
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13
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Vasconcelos FF, Castro DS. Coordinating neuronal differentiation with repression of the progenitor program: Role of the transcription factor MyT1. NEUROGENESIS 2017. [DOI: 10.1080/23262133.2017.1329683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Blitz IL, Paraiso KD, Patrushev I, Chiu WTY, Cho KWY, Gilchrist MJ. A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. Dev Biol 2016; 426:409-417. [PMID: 27475627 PMCID: PMC5596316 DOI: 10.1016/j.ydbio.2016.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/01/2016] [Accepted: 07/01/2016] [Indexed: 12/30/2022]
Abstract
Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog of the transcription factors for the diploid frog Xenopus tropicalis. We identify 1235 genes encoding DNA-binding transcription factors, comparable to the numbers found in typical mammalian species. In detail, the repertoire of X. tropicalis transcription factor genes is nearly identical to human and mouse, with the exception of zinc finger family members, and a small number of species/lineage-specific gene duplications and losses relative to the mammalian repertoires. We applied this resource to the identification of transcription factors differentially expressed in the early gastrula stage embryo. We find transcription factor enrichment in Spemann's organizer, the ventral mesoderm, ectoderm and endoderm, and report 218 TFs that show regionalized expression patterns at this stage. Many of these have not been previously reported as expressed in the early embryo, suggesting thus far unappreciated roles for many transcription factors in the GRNs regulating early development. We expect our transcription factor catalog will facilitate myriad studies using Xenopus as a model system to understand basic biology and human disease.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - William T Y Chiu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
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15
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Lopez E, Berenguer M, Tingaud-Sequeira A, Marlin S, Toutain A, Denoyelle F, Picard A, Charron S, Mathieu G, de Belvalet H, Arveiler B, Babin PJ, Lacombe D, Rooryck C. Mutations in MYT1, encoding the myelin transcription factor 1, are a rare cause of OAVS. J Med Genet 2016; 53:752-760. [PMID: 27358179 DOI: 10.1136/jmedgenet-2016-103774] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/26/2016] [Accepted: 06/01/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder involving first and second branchial arches derivatives, mainly characterised by asymmetric ear anomalies, hemifacial microsomia, ocular defects and vertebral malformations. Although numerous chromosomal abnormalities have been associated with OAVS, no causative gene has been identified so far. OBJECTIVES We aimed to identify the first causative gene for OAVS. METHODS As sporadic cases are mostly described in Goldenhar syndrome, we have performed whole exome sequencing (WES) on selected affected individuals and their unaffected parents, looking for de novo mutations. Candidate gene was tested through transient knockdown experiment in zebrafish using a morpholino-based approach. A functional test was developed in cell culture in order to assess deleterious consequences of mutations. RESULTS By WES, we identified a heterozygous nonsense mutation in one patient in the myelin transcription factor 1 (MYT1) gene. Further, we detected one heterozygous missense mutation in another patient among a cohort of 169 patients with OAVS. This gene encodes the MYT1. Functional studies by transient knockdown of myt1a, homologue of MYT1 in zebrafish, led to specific craniofacial cartilage alterations. Treatment with all-trans retinoic acid (RA), a known teratogenic agent causing OAVS, led to an upregulation of cellular endogenous MYT1 expression. Additionally, cellular wild-type MYT1 overexpression induced a downregulation of RA receptor β (RARB), whereas mutated MYT1 did not. CONCLUSION We report MYT1 as the first gene implicated in OAVS, within the RA signalling pathway.
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Affiliation(s)
- Estelle Lopez
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Marie Berenguer
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Angèle Tingaud-Sequeira
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Sandrine Marlin
- Département de Génétique, Hôpital Universitaire Necker-Enfants-Malades, Centre de Référence des Surdités Génétiques, Paris, France
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, Centre Hospitalier Universitaire, Tours, France
| | - Françoise Denoyelle
- Service d'ORL pédiatrique et de chirurgie cervicofaciale, Hôpital Universitaire Necker-Enfants-Malades, Centre de Référence des malformations ORL rares, Paris, France
| | - Arnaud Picard
- Service de chirurgie maxillo-faciale, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Sabine Charron
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Guilaine Mathieu
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Harmony de Belvalet
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Benoit Arveiler
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France.,Service de Génétique Médicale, CHU de Bordeaux, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Bordeaux, France
| | - Patrick J Babin
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Didier Lacombe
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France.,Service de Génétique Médicale, CHU de Bordeaux, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Bordeaux, France
| | - Caroline Rooryck
- University of Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France.,Service de Génétique Médicale, CHU de Bordeaux, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Bordeaux, France
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16
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Besold AN, Michel SLJ. Neural Zinc Finger Factor/Myelin Transcription Factor Proteins: Metal Binding, Fold, and Function. Biochemistry 2015; 54:4443-52. [DOI: 10.1021/bi501371a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Angelique N. Besold
- Department of Pharmaceutical
Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Sarah L. J. Michel
- Department of Pharmaceutical
Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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17
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Luo Y, North JA, Poirier MG. Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA. Methods 2014; 70:108-18. [PMID: 25304387 DOI: 10.1016/j.ymeth.2014.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/20/2022] Open
Abstract
Site specific DNA binding complexes must bind their DNA target sites and then reside there for a sufficient amount of time for proper regulation of DNA processing including transcription, replication and DNA repair. In eukaryotes, the occupancy of DNA binding complexes at their target sites is regulated by chromatin structure and dynamics. Methodologies that probe both the binding and dissociation kinetics of DNA binding proteins with naked and nucleosomal DNA are essential for understanding the mechanisms by which these complexes function. Here, we describe single-molecule fluorescence methodologies for quantifying the binding and dissociation kinetics of transcription factors at a target site within DNA, nucleosomes and nucleosome arrays. This approach allowed for the unexpected observation that nucleosomes impact not only binding but also dissociation kinetics of transcription factors and is well-suited for the investigation of numerous DNA processing complexes that directly interact with DNA organized into chromatin.
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Affiliation(s)
- Yi Luo
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Justin A North
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, United States; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210-1117, United States.
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18
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Lee SJ, Michel SLJ. Structural metal sites in nonclassical zinc finger proteins involved in transcriptional and translational regulation. Acc Chem Res 2014; 47:2643-50. [PMID: 25098749 DOI: 10.1021/ar500182d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc finger (ZF) proteins are a large family of metalloproteins that utilize zinc for structural purposes. Zinc coordinates to a combination of cysteine thiol and histidine imidazole residues within the ZF polypeptide sequence resulting in a folded and functional protein. Initially, a single class of ZFs were identified. These ZFs, now referred to as the "classical" ZFs, utilize a Cys2His2 (CCHH) ligand set to bind zinc. Upon Zn coordination, the classical ZFs fold into a structure made up of an α helix and an antiparallel β sheet. When folded, classical ZFs recognize and bind to specific DNA targets and function as transcription factors. With the advent of genome sequencing and proteomics, many additional classes of ZFs were identified based upon their primary amino acid sequences. At least 13 additional classes of ZFs are known, and collectively these "nonclassical" ZFs differ in the ligand set involved in Zn(II) coordination, the organization of the ligands within the polypeptide sequence and the macromolecular targets. Some nonclassical ZFs are DNA binding "transcription factors", while others are involved in RNA regulation and protein recognition. Much less is known about these nonclassical ZFs with regards to the roles of metal coordination in fold and function. This Account focuses on our laboratory's efforts to characterize two families of "nonclassical" ZFs: the Cys3His (or CCCH) ZF family and the Cys2His2Cys (or CCHHC) ZF family. Our work on the CCCH ZF family has focused on the protein Tristetraprolin (TTP), which is a key protein in regulating inflammation. TTP contains two CCCH domains that were proposed to be ZFs based upon their sequence. We have shown that while this protein can coordinate Zn(II) at the CCCH sites, it can also coordinate Fe(II) and Fe(III). Moreover, the zinc and iron bound forms of TTP are equally adept at discriminating between RNA targets, which we have demonstrated via a fluorescence anisotropy based approach. Thus, CCCH type ZFs appear to be promiscuous with respect to metal preference and a role for iron coordination in CCCH ZF function is proposed. The CCHHC family of ZFs is a small family of nonclassical ZFs that are essential for the development of the central nervous system. There are three ZFs in this family: neural zinc finger factor-1 (NZF-1), myelin transcription factor-1 (MyT1), and suppressor of tumorgenicity 18 (ST18). All three proteins contain multiple clusters of "CCHHC" domains, which are all predicted to be Zn binding domains. We have focused on a tandem-CCHHC domain construct of NZF-1, which recognizes β-RARE DNA, and we have identified key residues required for DNA recognition. Unlike classical ZFs, for which a few conserved residues are required for DNA recognition, the CCHHC class of ZFs utilize a few nonconserved residues to drive DNA recognition leading us to propose a new paradigm for ZF/DNA binding.
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Affiliation(s)
- Seung Jae Lee
- Department
of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Sarah L. J. Michel
- Department
of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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19
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Besold AN, Amick DL, Michel SLJ. A role for hydrogen bonding in DNA recognition by the non-classical CCHHC type zinc finger, NZF-1. MOLECULAR BIOSYSTEMS 2014; 10:1753-6. [PMID: 24820620 DOI: 10.1039/c4mb00246f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally important hydrogen bonding interaction.
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Affiliation(s)
- Angelique N Besold
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA.
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